Metagenomics as a tool for the investigation of uncultured microorganisms

[1]  A. Clark.  The Human Microbiome. , 2017, The American journal of nursing.

[2]  Christian Rinke,et al.  Impact of single-cell genomics and metagenomics on the emerging view of extremophile “microbial dark matter” , 2014, Extremophiles.

[3]  Tanja Woyke,et al.  Obtaining genomes from uncultivated environmental microorganisms using FACS–based single-cell genomics , 2014, Nature Protocols.

[4]  Alan Walker,et al.  Adding genomic 'foliage' to the tree of life , 2014, Nature Reviews Microbiology.

[5]  Stephen R Quake,et al.  Dissecting genomic diversity, one cell at a time , 2013, Nature Methods.

[6]  B. Baker,et al.  Omic Approaches in Microbial Ecology: Charting the Unknown , 2013 .

[7]  Natalia N. Ivanova,et al.  Insights into the phylogeny and coding potential of microbial dark matter , 2013, Nature.

[8]  Christian A. Ross,et al.  Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage , 2013, Nature Communications.

[9]  J. Dodsworth,et al.  Pyrosequencing Reveals High-Temperature Cellulolytic Microbial Consortia in Great Boiling Spring after In Situ Lignocellulose Enrichment , 2013, PloS one.

[10]  P. Blainey.  The future is now: single-cell genomics of bacteria and archaea. , 2013, FEMS microbiology reviews.

[11]  Monzoorul Haque Mohammed,et al.  Classification of metagenomic sequences: methods and challenges , 2012, Briefings Bioinform..

[12]  R. Stepanauskas.  Single cell genomics: an individual look at microbes. , 2012, Current opinion in microbiology.

[13]  N. Ravin,et al.  The impact of genomics on research in diversity and evolution of archaea , 2012, Biochemistry (Moscow).

[14]  R. Lasken.  Genomic sequencing of uncultured microorganisms from single cells , 2012, Nature Reviews Microbiology.

[15]  Alice Carolyn McHardy,et al.  Taxonomic binning of metagenome samples generated by next-generation sequencing technologies , 2012, Briefings Bioinform..

[16]  P. Chain,et al.  Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. , 2012, Current opinion in biotechnology.

[17]  M. Hattori,et al.  A Deeply Branching Thermophilic Bacterium with an Ancient Acetyl-CoA Pathway Dominates a Subsurface Ecosystem , 2012, PloS one.

[18]  Eric P. Nawrocki,et al.  An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea , 2011, The ISME Journal.

[19]  R. Stepanauskas,et al.  New Abundant Microbial Groups in Aquatic Hypersaline Environments , 2011, Scientific reports.

[20]  Hideaki Tanaka,et al.  MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads , 2011, BCB '11.

[21]  J. Banfield,et al.  De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities , 2011, The ISME Journal.

[22]  Kang Ning,et al.  Saliva microbiomes distinguish caries-active from healthy human populations , 2011, The ISME Journal.

[23]  J. Inman,et al.  TheViral MetaGenome Annotation Pipeline(VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data , 2011, Standards in genomic sciences.

[24]  Siu-Ming Yiu,et al.  Meta-IDBA: a de Novo assembler for metagenomic data , 2011, Bioinform..

[25]  P. Forterre,et al.  Phylogeny and evolution of the Archaea: one hundred genomes later. , 2011, Current opinion in microbiology.

[26]  N. Ravin,et al.  Uncultured archaea dominate in the thermal groundwater of Uzon Caldera, Kamchatka , 2011, Extremophiles.

[27]  N. Ravin,et al.  Molecular analysis of microbial diversity in the Zavarzin Spring, Uzon Caldera, Kamchatka , 2011, Microbiology.

[28]  M. Hattori,et al.  Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group , 2010, Nucleic acids research.

[29]  Doug Hyatt,et al.  Enigmatic, ultrasmall, uncultivated Archaea , 2010, Proceedings of the National Academy of Sciences.

[30]  Daphne Koller,et al.  Genovo: De Novo Assembly for Metagenomes , 2010, RECOMB.

[31]  Christopher L. Hemme,et al.  GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity , 2010, The ISME Journal.

[32]  C. Schleper,et al.  Diversity and abundance of Korarchaeota in terrestrial hot springs of Iceland and Kamchatka , 2010, The ISME Journal.

[33]  R. Amann,et al.  Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group. , 2010, Environmental microbiology.

[34]  James R. Cole,et al.  Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment , 2009, The ISME Journal.

[35]  Brian C. Thomas,et al.  Community-wide analysis of microbial genome sequence signatures , 2009, Genome Biology.

[36]  K. Nelson,et al.  Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases , 2009, Proceedings of the National Academy of Sciences.

[37]  Andreas Wilke,et al.  phylogenetic and functional analysis of metagenomes , 2022 .

[38]  E. Koonin,et al.  A korarchaeal genome reveals insights into the evolution of the Archaea , 2008, Proceedings of the National Academy of Sciences.

[39]  D. Relman,et al.  Linking Microbial Phylogeny to Metabolic Activity at the Single-Cell Level by Using Enhanced Element Labeling-Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (EL-FISH) and NanoSIMS , 2008, Applied and Environmental Microbiology.

[40]  Natalia N. Ivanova,et al.  Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite , 2007, Nature.

[41]  R. Knight,et al.  The Human Microbiome Project , 2007, Nature.

[42]  I-Min A. Chen,et al.  IMG/M: a data management and analysis system for metagenomes , 2007, Nucleic Acids Res..

[43]  J. Neufeld,et al.  Witnessing the last supper of uncultivated microbial cells with Raman-FISH , 2007, The ISME Journal.

[44]  Philip Hugenholtz,et al.  Lineages of Acidophilic Archaea Revealed by Community Genomic Analysis , 2006, Science.

[45]  K. Konstantinidis,et al.  The bacterial species definition in the genomic era , 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.

[46]  A. Teske,et al.  Stratified Communities of Active Archaea in Deep Marine Subsurface Sediments , 2006, Applied and Environmental Microbiology.

[47]  Michael Wagner,et al.  Linking microbial community structure with function: fluorescence in situ hybridization-microautoradiography and isotope arrays. , 2006, Current opinion in biotechnology.

[48]  J. R. Meer.  Analytics with engineered bacterial bioreporter strains and systems. , 2006 .

[49]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[50]  J. Banfield,et al.  Community Proteomics of a Natural Microbial Biofilm , 2005, Science.

[51]  J. Handelsman.  Metagenomics: Application of Genomics to Uncultured Microorganisms , 2004, Microbiology and Molecular Biology Reviews.

[52]  J. Handelsman,et al.  Metagenomics: genomic analysis of microbial communities. , 2004, Annual review of genetics.

[53]  Daniel Rokhsar,et al.  Reverse Methanogenesis: Testing the Hypothesis with Environmental Genomics , 2004, Science.

[54]  J. Banfield,et al.  Acid mine drainage biogeochemistry at Iron Mountain, California , 2004, Geochemical transactions.

[55]  O. White,et al.  Environmental Genome Shotgun Sequencing of the Sargasso Sea , 2004, Science.

[56]  J. Banfield,et al.  Community structure and metabolism through reconstruction of microbial genomes from the environment , 2004, Nature.

[57]  K. Schleifer,et al.  Oligonucleotide Microarray for 16S rRNA Gene-Based Detection of All Recognized Lineages of Sulfate-Reducing Prokaryotes in the Environment , 2002, Applied and Environmental Microbiology.

[58]  N. Pace,et al.  Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[59]  E. Delong,et al.  Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon , 1996, Journal of bacteriology.

[60]  K. Schleifer,et al.  Phylogenetic identification and in situ detection of individual microbial cells without cultivation. , 1995, Microbiological reviews.

[61]  E. Delong,et al.  Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing , 1991, Journal of bacteriology.

[62]  C. Woese.  Bacterial evolution , 1987, Microbiological reviews.

[63]  N. Pace,et al.  Analysis of Hydrothermal Vent-Associated Symbionts by Ribosomal RNA Sequences , 1984, Science.

[64]  Stephen R Quake,et al.  Optofluidic cell selection from complex microbial communities for single-genome analysis. , 2013, Methods in enzymology.

[65]  S. Turner,et al.  Real-time DNA sequencing from single polymerase molecules. , 2010, Methods in enzymology.

[66]  A. Teske,et al.  Uncultured archaea in deep marine subsurface sediments: have we caught them all? , 2008, The ISME Journal.

[67]  B. Ahring,et al.  Archaeal diversity in Icelandic hot springs. , 2007, FEMS microbiology ecology.

[68]  R. Garrett,et al.  Archaea : evolution, physiology, and molecular biology , 2007 .

[69]  M. Freidin,et al.  Russian Journal of Genetics , 2002 .

[70]  John A. Hertz,et al.  Modeling Genetic Regulatory Dynamics in Neural Development , 2002, J. Comput. Biol..